Transcriptome Analysis Reveals the Effect of Oyster Mushroom Spherical Virus Infection in Pleurotus ostreatus
Abstract
:1. Introduction
2. Results
2.1. Transcriptome Data Assembly Results
2.2. Expression Analysis
2.3. Differential Gene Analysis
2.4. KOG Functional Enrichment Analysis of DEGs
2.5. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes Functional Enrichment Analysis of DEGs
2.6. Quantitative Reverse Transcription-PCR Validation of DEGs
2.7. Effect of OMSV Infection on CAZymes
3. Discussion
4. Materials and Methods
4.1. RNA Extraction
4.2. Reverse Transcription PCR
4.3. cDNA Library Preparation and Illumina Sequencing
4.4. Data Processing and Differential Expression Analysis
4.5. Functional Analysis of DEGs
4.6. Quantitative RT-PCR Validation
4.7. Measurement of Enzyme Activity
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Samples | Clean Reads | Clean Bases | GC Content | % ≥ Q30 |
---|---|---|---|---|
Mock-1 | 20,965,286 | 6,276,707,342 | 53.67% | 92.68% |
Mock-2 | 23,424,577 | 7,016,262,210 | 53.80% | 94.51% |
Mock-3 | 22,083,023 | 6,613,712,742 | 53.68% | 92.63% |
OMSV-1 | 24,515,659 | 7,343,439,530 | 54.18% | 94.47% |
OMSV-2 | 24,050,037 | 7,202,732,604 | 54.08% | 94.54% |
OMSV-3 | 22,548,293 | 6,753,639,986 | 54.24% | 94.88% |
Pathway | DEGs with Pathway Annotation | Pathway ID | p-Value |
---|---|---|---|
Glyoxylate and dicarboxylate metabolism | 6 (6.12%) | ko00630 | 0.000953 |
Glycine, serine, and threonine metabolism | 9 (9.18%) | ko00260 | 0.000997 |
Fatty acid biosynthesis | 5 (5.10%) | ko00061 | 0.003113 |
Penicillin and cephalosporin biosynthesis | 2 (2.04%) | ko00311 | 0.005509 |
D-Arginine and D-ornithine metabolism | 2 (2.04%) | ko00472 | 0.005509 |
Propanoate metabolism | 5 (5.10%) | ko00640 | 0.008949 |
One carbon pool by folate | 3 (3.06%) | ko00670 | 0.010096 |
Phenylalanine, tyrosine, and tryptophan biosynthesis | 3 (3.06%) | ko00400 | 0.014425 |
Non-homologous end-joining | 3 (3.06%) | ko03450 | 0.014425 |
Cutin, suberine, and wax biosynthesis | 2 (2.04%) | ko00073 | 0.018137 |
Genes | Annotation | log2FoldChange | 2−ΔΔCt |
---|---|---|---|
g1073569 | Methylenetetrahydrofolate dehydrogenase | −1.92 | 0.97 |
g1052256 | S-adenosylmethionine synthetase | −1.48 | 0.34 |
g1047319 | Polyketide synthase | −3.64 | 0.80 |
g1073665 | Aryl-alcohol dehydrogenase | −1.93 | 0.05 |
g1088328 | Enoyl-(Acyl carrier protein) reductase | 1.70 | 2.16 |
g1113424 | Cytochrome P450 | −2.14 | 0.18 |
g1074848 | Chitinase | 1.75 | 1.32 |
g1077485 | Nicotinate-nucleotide pyrophosphorylase | −0.70 | 0.85 |
g1088664 | 1,3-beta-glucosidase | 0.66 | 1.26 |
g1103527 | Beta-glucan synthesis-associated protein | −0.82 | 0.64 |
g1036297 | Polysaccharide lyase family 8 protein | 1.03 | 2.29 |
g51725 | Laccase | −0.60 | 0.77 |
g1067151 | Chitin synthase | −2.41 | 0.09 |
g1044280 | Lipase | 1.96 | 1.06 |
g1046093 | 50S ribosome-binding GTPase | 3.50 | 5.81 |
Gene ID | Forward Primer (5′→3′) | Reverse Primer (5′→3′) | Size (bp) |
---|---|---|---|
g1073569 | GAAGTCGGAGGCCGTATCAG | CATACGTCGAGGAATCGGGG | 103 |
g1052256 | TGGTCACCACTGTCGTCTTG | CGATGCGTGTAGAAGGTGGT | 114 |
g1047319 | TGACCGCTCGCAGACAAAT | CTTCTCGATAAGCTCAGCCTTGG | 74 |
g1088328 | TTGTTACCGGCCAGGTGATG | AAACATCGAGTTTGCATCGCT | 76 |
g1044280 | TTTCTGGGTTTCCACCACCC | TCTTGGCCTGGACAGGAAAC | 80 |
g1073665 | ACAGTTCATCGGTGAGTGGG | GCCGTGTACTTGGTCGAGATA | 72 |
g1067151 | GGGAGCTGCTTTGGATGAGT | ACTGTGAGGCACAGCGATAG | 86 |
g1113424 | AGTGGCAGGTTCTTGGTCTG | CAAAGGTAAGGCGAACGACG | 115 |
g1046093 | TGGATCTTCCTGAAACCGCC | TAGCACGAGGGAAGAGTTAAGTG | 145 |
g1074848 | TTCGGGCACATCTTATTGGGG | ATCGATGGAATCGTCCTGGC | 106 |
g1077485 | ATGTTCGTCGTGGCACTTCT | CAGCGATATGAGAGTGGCGT | 100 |
g1088664 | CCCATCGTCTCAGCCTTCAA | ACTCTACTCACGGTCTGCGA | 91 |
g1103527 | ACCTCGGTTTCTCTCCCAGG | GCTCTGCCGAGATTACCCAT | 80 |
g1036297 | TGGTACACCGTGGACGCAAT | CATTCTGTGTTGACGGTGCG | 70 |
g51725 | GGATGGATACAGTCGCCAGG | CAATCTGAAGGTGTCGCCCT | 88 |
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Wang, Y.; Yan, J.; Song, G.; Song, Z.; Shi, M.; Hu, H.; You, L.; Zhang, L.; Wang, J.; Liu, Y.; et al. Transcriptome Analysis Reveals the Effect of Oyster Mushroom Spherical Virus Infection in Pleurotus ostreatus. Int. J. Mol. Sci. 2024, 25, 9749. https://doi.org/10.3390/ijms25179749
Wang Y, Yan J, Song G, Song Z, Shi M, Hu H, You L, Zhang L, Wang J, Liu Y, et al. Transcriptome Analysis Reveals the Effect of Oyster Mushroom Spherical Virus Infection in Pleurotus ostreatus. International Journal of Molecular Sciences. 2024; 25(17):9749. https://doi.org/10.3390/ijms25179749
Chicago/Turabian StyleWang, Yifan, Junjie Yan, Guoyue Song, Zhizhong Song, Matthew Shi, Haijing Hu, Lunhe You, Lu Zhang, Jianrui Wang, Yu Liu, and et al. 2024. "Transcriptome Analysis Reveals the Effect of Oyster Mushroom Spherical Virus Infection in Pleurotus ostreatus" International Journal of Molecular Sciences 25, no. 17: 9749. https://doi.org/10.3390/ijms25179749